A Comprehensive Review of Protein Biomarkers for Invasive Lung Cancer

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

WELL DONE!A COMPLET WORK.NOTHING TO DISCUSS.JUST A THOUGHT : ADD THE TNM AND WHO  CLASSIFICATION

Author Response

Dear Editor,

We would thank the reviewers for their time and comments, which helped us improve the revised version of the manuscript.

Reviewer #1 recommended that we include the most commonly used classifications of lung cancer, specifically the World Health Organization (WHO) classification and the TNM classification. In response to this suggestion, we added two new paragraphs to the manuscript, which provide a detailed description of both classifications (see page 2, lines 40-45 and 53-64, respectively).

Sincerely,
MEZENTSEV, Alexandre, PhD

Reviewer 2 Report

Comments and Suggestions for Authors

 

Protein Biomarkers for Invasive Lung Cancer

The authors present a review paper on lung cancer proteomics, focusing on metastasis and invasiveness. Some comments are provided below.

Title / Abstract

The paper would be more readable if it set out from the beginning that it is a review paper, rather than experimental research. Suggest to alter the title to "A review of Protein Biomarkers for Invasive Lung Cancer"

Within the Abstract, suggest in the last sentence "This review paper aims to discuss the advantages and limitations of protein biomarkers of invasiveness in lung cancer, to assess their prognostic value, and propose novel biomarker candidates."

Introduction

The opening sentence might be better written as “Cancer is a life-threatening condition, with the outlook for patients deteriorating as the disease progresses to metastasis, the process by which cancer cells away from the primary tumor to colonize distant organs.”

It might be helpful in the Introduction to briefly discuss the growth in proteomics technology and also in machine learning, which is increasing the number of studies on protein biomarkers very rapidly. This underlines the importance of synthesising the latest research in the area in this review paper.

Methods

After Introduction, the authors should add a brief description of the literature review process and method used, under a new heading, 2. Methods. For example, the databases that the researchers looked at, the search strings employed (including Boolean operators if appropriate), and the inclusion and exclusion criteria, for example what years the authors considered relevant. It would be nice if the authors could also include a PRISMA flowchart if possible, but this is not essential if the review is not intended to be systematic.

(https://doi.org/10.1177/1937586717747384)

Under the heading “Biomarkers for invasive lung cancer”, it would be helpful to add a table after the first paragraph, at line 181. This could list the proposed biomarkers for each subsection, and provide some additional information on which pathways the proteins are associated or the Uniprot link (or the gene card if it is better). This might help the reader have a quick summary of the following section, which is quite long.

Biomarker          Full name                           Link

MAPK15              Mitogen-activated protein kinase 15    https://www.uniprot.org/uniprotkb/Q8TD08/entry

LOXL2                  Lysyl oxidase homolog 2                             https://www.uniprot.org/uniprotkb/Q9Y4K0/entry

Limitations section

The authors do not discuss challenges and limitations in the field in an organised way, especially the general problems around translation of biomarker research to clinical practice. It would help the reader very much if a short section dedicated to the limitations could be added under a new heading, Limitations of biomarker research, immediately before Conclusions. Otherwise the reader might reasonably think that with so many biomarkers available, why is there not a biomarker based blood test already?

Specific challenges that the authors could cover in this short paragraph could include:

Proteomics studies produce high dimensional data, sometimes with thousands of potential biomarkers. This increases the chances of false discoveries, especially given the low prior odds of finding ‘true’ relationships. This issue of low prior odds meaning that many preliminary discoveries will be false is well described (https://doi.org/10.1371/journal.pmed.0020124)

Cancer studies and other proteomics works often include idealised case versus control comparisons, which means that biomarkers of general poor  health can be mixed in with biomarkers that are specific to a single condition. Especially with machine learning models for high dimensional data, that are built using idealised case-control cohorts, this can lead to specificity of biomarkers being overstated (https://doi.org/10.1016/j.heliyon.2023.e22604)

It should also be noted that proteomics as a discipline has made substantial progress in reproducibility and accuracy in recent years, but still faces a number of technical challenges around proteoform identification, solubility of proteins, mass spectrometry dynamic range and proteome complexity. Continued progress in these technical areas will be vital to further improve the biomarker discovery process (https://doi.org/10.1021/jasms.1c00099)

Overall, however, the article is well written and appears to give a good summary of recent biomarker work.

 

Comments on the Quality of English Language

No comments on the English Language which is generally of a good standard.

Author Response

Dear Editor,

We would thank the reviewers for their time and comments, which helped us improve the revised version of the manuscript.

We received seven comments from Reviewer #2, which we address below.

In COMMENT #1, the reviewer suggested making the title of the manuscript more informative and proposed an alternative. We agreed with the reviewer and changed the title from “Protein Biomarkers for Invasive Lung Cancer” to “A Comprehensive Review of Protein Biomarkers for Invasive Lung Cancer” (lines 2-3).

In COMMENT #2, the reviewer recommended revising the Abstract. We agreed and made changes to the conclusive remark, which now reads: “This review paper aims to discuss the advantages and limitations of protein biomarkers of invasiveness in lung cancer, to assess their prognostic value, and propose novel biomarker candidates” (lines 21-23).

In COMMENT #3, the reviewer suggested clarifying the opening sentence of the Introduction. In response, we made the necessary changes and rewrote the sentence as follows: “Cancer is a life-threatening condition with the outlook for patients deteriorating as the disease progresses to metastasis, the process by which cancer cells move away from the primary tumor to colonize distant organs" (lines 28-30).

In COMMENT #4, the reviewer suggested that we discuss the growth in proteomics technology and machine learning. We have addressed this comment by adding a new paragraph to the Introduction section (lines 103-116, page 3), which reads: “Academic and clinical scientists have increasingly recognized the potential benefits of proteomic approaches, which include mass spectrometry and alternative technologies [32]. Established protein biomarkers for lung cancer are highly effective in diagnosing the disease, monitoring the response to therapy, and evaluating treatment outcomes [33,34]. The development of machine learning techniques has significantly expanded the possibilities in this field [35,36]. The proposed computer models analyze an extensive array of parameters (features) to classify high-throughput data derived from large cohorts of patients. Recent publications have numerous examples describing the successful integration of machine learning algorithms into biomarker research [37,38]. In the future, the incorporation of these innovative methods into broader interdisciplinary projects led by consortia of researchers will be a common practice. These comprehensive studies will link multi-omic data with the results obtained by traditional methods, thereby optimizing the selection of treatment options for each patient to achieve the best possible outcome.”

In COMMENT #5, the reviewer suggested that we add a new section to the manuscript, entitled "Methods", which would provide a brief description of the literature review process and the approaches used to select and evaluate the data. We have addressed this comment by adding the requested section, which now appears after the "Introduction" (lines 130-156, page 4-5). This new section provides a clear overview of our methodology, ensuring transparency and reproducibility.

Regarding the reviewer's suggestion to include a PRISMA flowchart, we would like to clarify that our manuscript is not a systematic review, and therefore, we did not hear before about the PRISMA guidelines. As we do not have prior experience with PRISMA, we have not included a flowchart with the updated version. However, we are confident that the added "Methods" section provides sufficient information about our literature review process and data evaluation approaches.

In Comment #6, the reviewer suggested that we create a list of proposed biomarkers for each subsection and place it at the beginning of Section 5, "Biomarkers for invasive lung cancer". We have addressed this comment by preparing the requested table and adding it to the manuscript (lines 242-245, page 7).

In Comment #7, the reviewer proposed that we introduce a new section to the manuscript to discuss the limitations of biomarkers research, specifically the challenges of translating biomarker research into clinical practice. We have incorporated this suggestion into a new section, entitled "6. Limitations and perspectives of biomarkers research". In this section, we also address the request from Reviewer #2 to share our opinion on the most adequate technology for detecting protein-based biomarkers in diagnostic routine practice. Our response to Reviewer #1's comment can be found in lines 1068-1118 (pages 32-33) and lines 1166-1171 (pages 33-34).

Sincerely,
MEZENTSEV, Alexandre, PhD

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript able to investigate the most promising protein based biomarker represents a timley relevant manuscript available for the publication on this journal after minor suggestions

 

- In the introduction section, please, could the authors point on the clinical application of protein based biomarkers for the management of lung cancer patients

 

- In the manuscript, please, could the authors also add a brief description of most adequate technology to detect protein based biomarkers in diagnostic routine practice?

- Please, could the authors add a brief description of recent clinical insights  for each protein biomarker in the manuscript?

- Please, could the authors review figure 1-3 improving details and quality?

Comments on the Quality of English Language

Minor English revision should be approached to improve the readability of the manuscript

Author Response

Dear Editor,

We would thank the reviewers for their time and comments, which helped us improve the revised version of the manuscript.

We received four comments from reviewer #3.

In COMMENT #1, the reviewer suggested that we describe the clinical applications of protein-based biomarkers for the management of lung cancer patients and include this description in the Introduction section. In response, we prepared a brief overview of the clinical applications of biomarkers in lung cancer management and added it to the manuscript (lines 87-102, page 3). This new addition provides context for the importance of biomarkers in lung cancer care and sets the stage for the rest of the manuscript.

In COMMENT #2, the reviewer suggested that we briefly describe the most adequate technology for detecting protein-based biomarkers in diagnostic routine practice. In response, we prepared a concise description of a promising approach that we would recommend, along with a justification for our choice (lines 1119-1150, pages 33-34).

In COMMENT #3, the reviewer requested that we add a brief description of recent clinical insights for each protein biomarker discussed in the manuscript. In response, we would clarify that our review focuses on prospective protein biomarkers of invasive lung cancer, which, with rare exceptions, are not yet commonly used in routine clinical practice. For this reason, we have focused on their biological effects and explored how these proteins might contribute to epithelial-to-mesenchymal transition (EMT) and cell motility, rather than describing their clinical potential. The majority of the protein biomarkers we evaluated were identified in experimental studies, and many have likely not been investigated as biomarkers in registered clinical trials. Consequently, there is currently limited insight into their clinical utility, making it challenging to provide a comprehensive description of recent clinical insights for each biomarker.

In COMMENT #4, the reviewer suggested that we improve the details and quality of Figures 1-3, which were submitted with the non-revised version of the manuscript. In response to this comment, we have revised these figures using the "APEX PACE" software, which is recommended by the publishers for generating high-quality images suitable for publication. This software has enabled us to enhance the clarity and resolution of the figures, ensuring that they meet the required standards for publication.

Sincerely,
MEZENTSEV, Alexandre, PhD

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have comprehensively responded to the previous suggestions, and I am very appreciative of their hard work. There are some very minor points remaining in the new text, but otherwise, I believe that the manuscript can be accepted for publication.

Line 149, in the new Methods section, the authors say three databases were used, but only list two (PubMed and Web of Science)

Line 255: in the new table 1, should it be "prospective" instead of "perspective"?

Comments on the Quality of English Language

English fine, would benefit from a minor / quick grammar check at the Editorial Proof stage

Author Response

Dear Editor,

We have received two additional comments from Reviewer #2 and would like to respond to them.

Regarding Line 149 in the new Methods section, the reviewer requested that we correct the numbers/names of the databases we sourced. In response, we have revised the text to read: "The authors primarily focused on papers published between 2019 and May 2024 available from PubMed and Web of Science."

In Line 255, the reviewer suggested replacing the word "perspective" with "prospective". We have made the necessary change as requested.

Sincerely,

Mezentsev, Alexandre, PhD